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Chem 223 Course Outline
Chem 223 - Lectures

Spring 2012

NOTES:

  • The list of lecture shown below is still in progress and will be updated as we go along.
  • Lecture notes for each lecture can be obtained from the lecture notes download page.
  • Some lectures may be finished in less than one lecture period.  Some lectures will require two lecture periods to cover the material.

Lecture

Topic

Reference Text Reading

Go to Topics in Reading
List Below
0
  • Introduction to course & mass spectrometry
 Dass Chap 1 Intro articles
1
  • Mass spectrometry - the physics of ions in space
    • definition of mass spectrometry and a mass spectrometer
    • formation & acceleration of ions – basic equations
    • dispersion of ions in a magnetic field – basic equations
    • elementary focusing of beams
 Watson Chap 2.II.5.A  
2
  • Double focusing
    • electric fields and electrostatic focussing
    • combination of electrostatic and magnetic fields
    • mass resolution
 de Hoffmann Chap 2.5
Watson Chap 2.III.5.B
McCloskey Chap 2: pp 37-47, Chap 6, & Appendix 1 		Ion optics
3
  • Isotopes and ion abundances
    • exact mass calculations
    • calculating theoretical isotope distributions
    • calculating isotopomer distributions
 de Hoffmann Chap 6.3
McCloskey Appendix 4 		 
4
  • Time of flight (TOF)
 de Hoffmann Chap 2.4
Watson 2.III.1 		TOF
5
  • Quadrupole rod mass analyzer
 de Hoffmann Chap 2.1
Watson Chap 2.III.2 		Quads & ion traps
6
  • Detectors
    • Faraday cup
    • Electron multipliers & conversion dynodes
    • Multichannel plates
 Watson Chap 2.V
McCloskey Chap 3 		 
7
  • Electron impact (EI) ionization
    • ion source design
    • interpreting EI fragmentation spectra
 de Hoffmann Chap 1.1
Watson Chap 6
McCloskey Chap 1: pp 1-10 		 
8
  • Chemical ionization (CI)
    • mechanism
    • source design
    • negative chemical ionization (NCI)
 de Hoffmann Chap 1.2
Watson Chap 7
McCloskey Chap 1: pp 10-20 		CI
9
  • Vacuum systems
    • Vacuum pumps
    • Vacuum gauges
 Watson Chap 2.VI
McCloskey Chap 3 		Vacuum
10
  • Equations of vacuum: "the arithmetic of emptiness"
  • Simple sample introduction
    • gas & liquid "leaks", solid probes
   Vacuum
11a
  • GCMS interfaces & rudimentary LCMS interfaces
 de Hoffmann Chap 5.1
Watson Chap 4, 10, & 11.II
McCloskey Chap 5 		 
11b
  • GC &LC atmospheric pressure CI interfaces
 de Hoffmann Chap 1.12
Watson Chap 4 		APCI
12
  • Electrospray ionization (ESI)
  • Deconvolution of multiply charged envelopes
 de Hoffmann Chap 1.11
Watson Chap 8 		ESI
13
  • Surface ionization
    • fast atom bombardment (FAB)
    • matrix assisted laser desorption ionization (MALDI)
 de Hoffmann Chap 1.4
Watson Chap 9
McCloskey Chap 1: pp 21-37, Chap 8, Chap 9, & Appendix 3 		FAB
MALDI
14
  • 3D ion trap
 de Hoffmann Chap 2.1-2.2.1
Watson Chap 2.III.2.A 		Quads & ion traps
15
  • Fourier transform (FT) ion cyclotron resonance (ICR) MS
 de Hoffmann Chap 2.6
Watson Chap 2.III.6 		FTMS
16
  • Tandem mass spectrometry - MS/MS
    • Metastable ions & double focusing BE systems
    • post source decay (PSD)
    • CID
      • quadrupole triple-sector instruments
      • hybrids (QTOF)
      • ion trap & MSn
      • FTMS
      • TOF & TOF-TOF
 de Hoffmann Chap 4
Watson Chap 3
McCloskey Chap 6 & Chap 10 		MS/MS
17
  • Linear ion traps (LIT)
 de Hoffmann Chap 2.2.2
Watson Chap 2.III.2.B 		Quads & ion traps
18
  • Proteins, peptide sequencing & proteomics
    • MALDI/TOF
    • ESI
    • database searching
 de Hoffmann Chap 8.2
Watson Chap 12.1-3
McCloskey Chap 12 		Proteomics
19
  • The Orbitrap MS
 de Hoffmann Chap 2.3
Watson Chap 2.III.3 		Orbitrap
20
  • Electron capture dissociation (ECD) & electron transfer dissociation (ETD)
 Watson Chap 12.II.5 ECD
ETD

  • Reading List:

    • Almost all of the papers are obtainable on-line as a PDF. I prefer searching through PubMed for the authors, or you can go through the UVM Library library website to download the PDF files of articles.
    • References for which PDFs file are not available are shown in green
    • Books in the library are shown in maroon.
  • Reading keyed to lectures:
    • See syllabus for list of books and reference materials.
  • Introductory articles:
    • Price: Standard definitions of terms relating to mass spectrometry: A report from the Committee on Measurements and Standards of the American Society for Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2(4): 336-348, 1991.
    • Tutorial on Mass Spectrometry from the ASMS
    • WD Lehmann: Pictograms for experimental parameters in mass spectrometry. J. Am. Soc. Mass Spectrom. 8: 756-759, 1997.
  • Ion optics:
    • H Wollnik, Ion optics in mass spectrometers. J. Mass Spectrom.34: 991-1006, 1999 — although dry to read, this tutorial contains a variety of references for further reading.
  • Vacuum:
    • Saul Dushman, Scientific Foundations of Vacuum Technique, 2nd ed., New York, Wiley, 1962. Bailey Howe Library QC166 .D85 1962. Chapter 2: arithmetic of emptiness equations
  • Chemical ionization:
    • A. G. Harrison, Chemical Ionization Mass Spectrometry, 2nd ed., CRC Press, 1992. Bailey Howe Library QD96.M3 H37 1992. Chapters 2 & 4.
  • ESI:
    • E Gelpi: Interfaces for coupled liquid-phase separation/mass spectrometry techniques. An update on recent developments. J. Mass Spectrom. 37: 241-253, 2002.
    • RB Cole: Some tenets pertaining to electrospray ionization mass spectrometry. J. Mass Spectrom. 35: 763-772, 2000.
    • Cole, R.B.: Electrospray Ionization Mass Spectrometry, John Wiley & Sons, NY, 1997. Bailey Howe Library QP519.9.M3 E44 1997.
    • SJ Gaskell: Electrospray: Principles and practice. J. Mass Spectrom. 32: 677-688, 1997.
    • JB Fenn, J Rosell & CK Meng: In electrospray ionization, how much pull does an ion need to escape its droplet prison? J. Am. Soc. Mass Spectrom. 8: 1147-1157, 1997.
    • JF Banks, Jr. & CM Whitehouse: Electrospray ionization mass spectrometry. Methods Enzymol. 270: 486-519, 1996.
    • M Mann, CK Meng & JB Fenn: Interpreting mass spectra of multiply charged ions. Anal. Chem. 61: 1702-1708, 1989.
    • MH Amad, NB Cech, GS Jackson & CG Enke: Importance of gas-phase proton affinities in determining the electrospray ionization response for analytes and solvents. J. Mass Spectrom. 35: 784-789, 2000.
  • APCI:
    • EC Horning, MG Horning, DI Carroll, I Dzidic & RN Stillwell: New picogram detection system based on a mass spectrometer with an external ionization source at atmospheric pressure. Anal. Chem. 45: 936-943, 1973.
    • EC Horning, DI Carroll, I Dzidic, KD Haegele, S Lin, CU Oertli & RN Stillwell: Development and use of analytical systems based on mass spectrometry. Clin. Chem. 23: 13-21, 1977.
    • E Brewer & J Henion: Atmospheric pressure ionization LC/MS/MS techniques for drug disposition studies. J. Pharm. Sci. 87: 395-402, 1998.
  • Quadrupoles & ion traps:
    • MB Denton & PE Miller: The quadrupole mass filter: Basic operating concepts. J. Chem. Educ. 63: 617-622, 1986.
    • JJ Leary & RL Schmidt: Quadrupole mass spectrometers: An intuitive look at the math. J. Chem. Educ. 73: 1142-1145, 1996.
    • RE March: An introduction to quadrupole ion trap mass spectrometry. J.Mass Spectrom. 32: 351-369, 1997.
    • KR Jonscher & JR Yates, III: The quadrupole ion trap mass spectrometer--A small solution to a big challenge. Anal.Biochem. 244: 1-15, 1997.
    • G Stafford, Jr.: Ion trap mass spectrometry: A personal perspective. J. Am. Soc. Mass Spectrom. 13: 589-596, 2002.
    • RE March: Quadrupole ion traps. Mass Spectrom. Rev. 28: 961-989, 2009.
    • NV Konenkov, M Sudakov & DJ Douglas: Matrix methods for the calculation of stability diagrams in quadrupole mass spectrometry. J. Am. Soc. Mass Spectrom. 13: 597-613, 2002.
    • DJ Douglas: Linear quadrupoles in mass spectrometry. Mass Spectrom. Rev. 28: 937-960, 2009.
    • JW Hager: A new linear ion trap mass spectrometer. Rapid Commun. Mass Spectrom. 16: 512-526, 2002.
    • JC Schwartz, MW Senko & JE Syka: A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 13: 659-669, 2002.
    • JW Hager & JC Yves Le Blanc: Product ion scanning using a Q-q-Q linear ion trap (Q TRAP) mass spectrometer. Rapid Commun. Mass Spectrom. 17: 1056-1064, 2003.
    • FA Londry & JW Hager: Mass selective axial ion ejection from a linear quadrupole ion trap. J. Am. Soc. Mass Spectrom. 14: 1130-1147, 2003.
    • DJ Douglas, AJ Frank & D Mao: Linear ion traps in mass spectrometry. Mass Spectrom. Rev. 24: 1-29, 2005.
  • FTMS or FT-ICR
    • AG Marshall & PB Grosshans: Fourier transform ion cyclotron resonance mass spectrometry: The teenage years. Anal.Chem. 63: 215A-229A, 1991.
    • IJ Amster: Fourier transform mass spectrometry. J.Mass Spectrom. 31: 1325-1337, 1996.
    • AG Marshall, CL Hendrickson & GS Jackson: Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17: 1-35, 1998.
  • Orbitrap
    • A Makarov: Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal. Chem. 72: 1156-1162, 2000.
    • A Makarov, E Denisov, A Kholomeev, W Balschun, O Lange, K Strupat & S Horning: Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78: 2113-2120, 2006.
    • A Makarov, E Denisov, O Lange & S Horning: Dynamic range of mass accuracy in LTQ Orbitrap hybrid mass spectrometer. J. Am. Soc. Mass Spectrom. 17: 977-982, 2006.
    • M Scigelova & A Makarov: Orbitrap mass analyzer - overview and applications in proteomics. Proteomics 6: 16-21, 2006.
    • Q Hu, RJ Noll, H Li, A Makarov, M Hardman & RG Cooks: The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 40: 430-443, 2005.
    • RH Perry, RG Cooks & RJ Noll: Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom. Rev. 27: 661-699, 2008.
    • JV Olsen, LM de Godoy, G Li, B Macek, P Mortensen, R Pesch, A Makarov, O Lange, S Horning & M Mann: Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4: 2010-2021, 2005.
    • 1. JV Olsen, B Macek, O Lange, A Makarov, S Horning & M Mann: Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4: 709-712, 2007.
  • TOF:
    • Time-of-flight mass spectrometry: Instrumentation and applications in biological research. Robert J. Cotter ed. American Chemical Society, 1997. Dana: QC 454 M3 C847t 1997.
    • RJ Cotter: The new time-of-flight mass spectrometry. Anal. Chem. 71: 445A-451A, 1999.
    • J Fjeldsted: Time-of-flight mass spectrometry – A Technical Overview. published as a technical document by Agilent, 2003 — describes LC-TOF analyzers
    • M Guilhaus: Principles and instrumentation in time-of-flight mass spectrometry: Physical and instrumental concepts. J. Mass Spectrom. 30: 1519-1532, 1995.
    • M Vestal & P Juhasz: Resolution and mass accuracy in matrix-assisted laser desorption ionization time-of-flight. J.Am.Soc.Mass Spectrom. 9: 892-911, 1998.
    • Agilent video on the operation of the LC-TOF
  • MALDI:
    • JJ Lennon: Matrix assisted laser desorption ionization time-of-flight mass spectrometry. 1997.
    • M Karas, M Glückmann & J Schäfer: Ionization in matrix-assisted laser desorption/ionization: Singly charged molecular ions are the lucky survivors. J. Mass Spectrom. 35: 1-12, 2000.
    • M Glückmann & M Karas: The initial ion velocity and its dependence upon matrix, analyte, and preparation method in ultraviolet matrix-assisted laser desorption/ionization. J. Mass Spectrom. 34: 467-477, 1999.
    • RS Brown & JJ Lennon: Mass resolution improvement by incorporation of pulsed ion extraction in a matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometer. Anal.Chem. 67: 1998-2003, 1995.
    • DH Russell & RD Emondson: High-resolution mass spectrometry and accurate mass meaurements with emphasis on the characterization of peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectometry. J. Mass Spectrom. 32: 263-276, 1997.
  • FAB:
    • M Barber, RS Bordoll, GJ Elliott, RD Sedgwick & AN Tyler: Fast atom bombardment mass spectrometry. Anal. Chem. 54: 645A-657A, 1982.
  • MS/MS:
    • E de Hoffmann: Tandem mass spectrometry: A primer. J. Mass Spectrom. 31: 129-137, 1996.
    • B Spengler: Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 32: 1019-1036, 1997.
    • KF Medzihradszky, JM Campbell, MA Baldwin, AM Falick, P Juhasz, ML Vestal & AL Burlingame: The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72: 552-558, 2000.
    • IV Chernushevich, AV Loboda & BA Thomson: An introduction to quadrupole-time-of-flight mass spectrometry. J. Mass Spectrom. 36: 849-865, 2001.
  • Electron capture dissociation (ECD)
    • DM Horn, RA Zubarev & FW McLafferty: Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 97: 10313-10317, 2000.
    • RA Zubarev, DM Horn, EK Fridriksson, NL Kelleher, NA Kruger, MA Lewis, BK Carpenter & FW McLafferty: Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 72: 563-573, 2000.
    • RA Zubarev: Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom. Rev. 22: 57-77, 2003.
    • HJ Cooper, K Hakansson & AG Marshall: The role of electron capture dissociation in biomolecular analysis. Mass Spectrom. Rev. 24: 201-222, 2005.
    • MA McFarland, MJ Chalmers, JP Quinn, CL Hendrickson & AG Marshall: Evaluation and optimization of electron capture dissociation efficiency in fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 16: 1060-1066, 2005.
    • YO Tsybin, JP Quinn, OY Tsybin, CL Hendrickson & AG Marshall: Electron capture dissociation implementation progress in Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 19: 762-771, 2008.
  • Electron tranfer dissociation (ETD)
    • JE Syka, JJ Coon, MJ Schroeder, J Shabanowitz & DF Hunt: Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101: 9528-9533, 2004.
    • JJ Coon, B Ueberheide, JE Syka, DD Dryhurst, J Ausio, J Shabanowitz & DF Hunt: Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 102: 9463-9468, 2005.
  • Peptide fragmentation
    • RS Johnson, SA Martin, K Biemann, JT Stults & JT Watson: Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal. Chem. 59: 2621-2625, 1987.
    • B Paizs & S Suhai: Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24: 508-548, 2005.
    • AG Harrison: To b or not to b: the ongoing saga of peptide b ions. Mass Spectrom. Rev. 28: 640-654, 2009.
  • Proteomics:
    • JR Yates, III: Mass spectrometry and the age of the proteome. J. Mass Spectrom. 33: 1-19, 1998.
    • J Peng & SP Gygi: Proteomics: The move to mixtures. J. Mass Spectrom. 36: 1083-1091, 2001.
    • R Aebersold & M Mann: Mass spectrometry-based proteomics. Nature 422: 198-207, 2003.
    • D Figeys: Proteomics in 2002: a year of technical development and wide-ranging applications. Anal. Chem. 75: 2891-2905, 2003.
    • D Lin, DL Tabb & JR Yates, III: Large-scale protein identification using mass spectrometry. Biochim. Biophys. Acta 1646: 1-10, 2003.
    • H Steen & M Mann: The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5: 699-711, 2004.

Last modified January 16 2012 02:43 PM

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